I have a Super Joybox 5 Pro (adapter to use Playstation2 controllers on a PC), but sadly it isn't recognized by TFU:USE. Thankfully however I can use a free program called "Joy2Key" which allows me to map keys and so forth for the game. I haven't seized on the optimum setup yet though.
Really, there's nothing the 360 controller can do that a Dual Shock 2 can't, other than perhaps the analog triggers (which the game doesn't use anyway, right?).
Anyway, I'm running the game with the 1.2 patch now (didn't need the 1.1).
Get the latest official patches here: